*Target (protein/gene name): Protein phosphatase-beta, putative (P. vivax) *NCBI Gene # or RefSeq#: None available on PubChem *Protein ID (NP or XP #) or Wolbachia#: 269949 *Organism (including strain):Plasmodium vivax Etiologic Risk Group (see link below): R2 *Background/Disease Information (sort of like the Intro to your MiniResearch Write up): Plasmodium vivax is a protozoal parasite that is the main source of malaria. P. vivax is one of six species of malaria carriers that infect humans. Link to TDR Targetspage (if present):http://tdrtargets.org/targets/view?gene_id=269949 Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.) http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&primary_key=PVX_099685 Essentiality of this protein: Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Sterility; Source study: neb Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Growth Defect; Source study: neb Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Larval/Adult Lethal/Arrest; Source study: neb Gene/Ortholog: cel8553 (OG4_10586); Phenotype:Embryonic Lethal/Arrest; Source study: neb Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Embryonic Lethal/Arrest; Source study: wormbase Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Larval/Adult Lethal/Arrest; Source study: wormbase Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Sterility; Source study: wormbase Gene/Ortholog: Tb927.3.1240 (OG4_10586); Phenotype: significant loss of fitness in bloodstream forms (3 days); Source study: alsford Gene/Ortholog: Tb927.3.1240 (OG4_10586); Phenotype: significant loss of fitness in bloodstream forms (6 days); Source study: alsford Gene/Ortholog: Tb927.3.1240 (OG4_10586); Phenotype: significant loss of fitness in procyclic forms; Source study: alsford Gene/Ortholog: Tb927.3.1240 (OG4_10586); Phenotype: no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms; Source study: alsford
Complex of proteins?: N/a Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): 0.6
*EC#: 3.1.3.16 Link to BRENDA EC# page: www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.3.16 --Show screenshot of BRENDA enzyme mechanism schematic
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage: 100%
---- Max % Identities: 100%
---- % Positives: 100%
---- Chain used for homology: Chain A
Current Inhibitors: Expression Information (has it been expressed in bacterial cells): Purification Method: Image of protein (PyMol with features delineated and shown separately): *Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
MSNCLAPSPDCQLSDALNSKGNPTRPNESSERSERSEIGQSGQSIQNSQSNRNSQNDNSY MEKKKKERRSEKKTHSPEQVRQKGEKNYEQSEKKKKLSNDEGVQVSTCETFVNEDNYTTY ENLSVKELSDEEVFSENEYNKKIKRSQNSLLISKEFYDFLVSNDDDQVSEKCTKNDARFE ELLQSEANSPPATCSTKVSHNVDEWINKLLKCELLHIEEVKLMCTLLRDILKEEPNCVQV SVPVTVAGDIHGQFYDLLELFHIGGFPPDVNYLFLGDYVDRGYYSCECFCLVACLKIKYP SRVTILRGNHESRQITKVYGFYDECMRKYDGDYNAWRYITDAFDYLPLTAIISNQIFCDH GGISPYLHTINQINNLDRFKEIPQDGPICDLLWSDPAGPEDGIIEGWKASPRGAGVVFSE ERTNAFLRLNKLSCICRAHQLVQDGFLWMHNDKVVTIFSAPNYCYRCGNSASLMLVDEYM EKDFVTFNTAPLRANAKALRRNVGYML *length of your protein in Amino Acids: 507aa Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 58046.1 Da Molar Extinction coefficient of your protein at 280 nm wavelength:
Ext. coefficient 62895 Abs 0.1% (=1 g/l) 1.084, assuming all pairs of Cys residues form cystines
Ext. coefficient 61770 Abs 0.1% (=1 g/l) 1.064, assuming all Cys residues are reduced TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it. *CDS Gene Sequence (paste as text only):
MLEVQPGLYFGGAAAVAEPDHLREAGITAVLTVDSEEPSFKAGPGVEDLWRLFVPALDKPETDLLSHLDRAVAFIGQARA EGRAVLVHSHAGVSRSVAIITAFLMKTDQLPFEKAYEKLQILKPEAKMNEGFEWQLKLYQAMGYEVDTSSAIYKQYRLQK VTEKYPE *GC% Content for gene: 6.5868263473054 *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): *GC% Content for gene (codon optimized): Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol) -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences): **
*NCBI Gene # or RefSeq#: None available on PubChem
*Protein ID (NP or XP #) or Wolbachia#: 269949
*Organism (including strain): Plasmodium vivax
Etiologic Risk Group (see link below): R2
*Background/Disease Information (sort of like the Intro to your MiniResearch Write up):
Plasmodium vivax is a protozoal parasite that is the main source of malaria. P. vivax is one of six species of malaria carriers that infect humans.
Link to TDR Targets page (if present): http://tdrtargets.org/targets/view?gene_id=269949
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)
http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&primary_key=PVX_099685
Essentiality of this protein:
Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Sterility; Source study: neb
Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Growth Defect; Source study: neb
Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Larval/Adult Lethal/Arrest; Source study: neb
Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Embryonic Lethal/Arrest; Source study: neb
Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Embryonic Lethal/Arrest; Source study: wormbase
Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Larval/Adult Lethal/Arrest; Source study: wormbase
Gene/Ortholog: cel8553 (OG4_10586); Phenotype: Sterility; Source study: wormbase
Gene/Ortholog: Tb927.3.1240 (OG4_10586); Phenotype: significant loss of fitness in bloodstream forms (3 days); Source study: alsford
Gene/Ortholog: Tb927.3.1240 (OG4_10586); Phenotype: significant loss of fitness in bloodstream forms (6 days); Source study: alsford
Gene/Ortholog: Tb927.3.1240 (OG4_10586); Phenotype: significant loss of fitness in procyclic forms; Source study: alsford
Gene/Ortholog: Tb927.3.1240 (OG4_10586); Phenotype: no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms; Source study: alsford
Complex of proteins?: N/a
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): 0.6
*EC#: 3.1.3.16
Link to BRENDA EC# page: www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.3.16
-- Show screenshot of BRENDA enzyme mechanism schematic
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
-- link to Sigma (or other company) page for assay (see Sigma links below)
http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/learning-center/assay-library/ec-number-iii.html
-- -or link (or citation) to paper that contains assay information
http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Enzyme_Assay/calcineurin.pdf
-- links to assay reagents (substrates) pages.
http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/General_Information/2/colipase.pdf
--- List cost and quantity of substrate reagents, supplier, and catalog #
Supplier: Sigma Aldrich
Catalog:
Price: $50
Structure Available (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model:
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage: 100%
---- Max % Identities: 100%
---- % Positives: 100%
---- Chain used for homology: Chain A
Current Inhibitors:
Expression Information (has it been expressed in bacterial cells):
Purification Method:
Image of protein (PyMol with features delineated and shown separately):
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
MSNCLAPSPDCQLSDALNSKGNPTRPNESSERSERSEIGQSGQSIQNSQSNRNSQNDNSY MEKKKKERRSEKKTHSPEQVRQKGEKNYEQSEKKKKLSNDEGVQVSTCETFVNEDNYTTY ENLSVKELSDEEVFSENEYNKKIKRSQNSLLISKEFYDFLVSNDDDQVSEKCTKNDARFE ELLQSEANSPPATCSTKVSHNVDEWINKLLKCELLHIEEVKLMCTLLRDILKEEPNCVQV SVPVTVAGDIHGQFYDLLELFHIGGFPPDVNYLFLGDYVDRGYYSCECFCLVACLKIKYP SRVTILRGNHESRQITKVYGFYDECMRKYDGDYNAWRYITDAFDYLPLTAIISNQIFCDH GGISPYLHTINQINNLDRFKEIPQDGPICDLLWSDPAGPEDGIIEGWKASPRGAGVVFSE ERTNAFLRLNKLSCICRAHQLVQDGFLWMHNDKVVTIFSAPNYCYRCGNSASLMLVDEYM EKDFVTFNTAPLRANAKALRRNVGYML
*length of your protein in Amino Acids: 507aa
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 58046.1 Da
Molar Extinction coefficient of your protein at 280 nm wavelength:
Ext. coefficient 62895 Abs 0.1% (=1 g/l) 1.084, assuming all pairs of Cys residues form cystines
Ext. coefficient 61770 Abs 0.1% (=1 g/l) 1.064, assuming all Cys residues are reduced
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
MLEVQPGLYFGGAAAVAEPDHLREAGITAVLTVDSEEPSFKAGPGVEDLWRLFVPALDKPETDLLSHLDRAVAFIGQARA EGRAVLVHSHAGVSRSVAIITAFLMKTDQLPFEKAYEKLQILKPEAKMNEGFEWQLKLYQAMGYEVDTSSAIYKQYRLQK VTEKYPE
*GC% Content for gene: 6.5868263473054
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
*GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
**